Welcome to the second post in our Senior Project blog topic series! Today, we are diving into the Senior Projects focused on research related to biology and/or medicinal sciences.

Research in these fields has the power to create huge social and economic change, be it increased quality of life, technological advancements in surgeries, treatments, and diagnosis, or even improving medical device manufacturing. These innovations depend on the breakthroughs and discoveries found in researching health, medicine, and biological science and thus we’re proud to have many students at BISV dedicate their research to this field.

One of today’s featured students, Amrita B., whose project focuses on the effectiveness of drug-eluting stents, recently shared some of her findings at a weekly lab meeting and recapped her experience in her blog, saying, “At first, it was honestly intimidating to present in front of some of the most qualified and knowledgeable people I have met. But I have realized that sharing is a part of the learning experience and leads to discussions that involve the exchanging of ideas and aids in progress.”

Another student, Lorne Z. is researching using machine learning to diagnose lung cancer, and he provided some updates on his project in his most recent blog post: “As I progress through this project, one observation I’ve made is that my initial idea of machine learning has changed. I used to think that machine learning was all about ideas and visualizing the neural networks. . . Overall, I’ve noticed that machine learning does not involve as much individual creation as I had suspected.”

Senior Project Advisor Dr. Anuradha Murthy, a Biology Subject Expert Teacher at BISV (and teacher of the very popular Biology of Cancer Capstone), worked with several students on their projects (which you can read through below), and provided her unique perspective on the process.

“It is amazing to see the creative and brilliant minds of the students at work. It keeps me relevant because I can see the topics and questions that they are interested in solving, world issues that they are passionate about, and concerns that they have at this stage in life. One of my students is trying to learn about bone surgeries because he has had a few, and being his advisor has made me so empathetic to his daily challenges. I see him through new eyes now; I never had the time when he took my classes to talk to him about his surgeries.”

Especially as these students are revving up for life in college, Dr. Murthy states that the completion of the Senior Project truly provides an invaluable edge as they begin their new journeys: “Senior Projects give the students a head start in the process of exploring what they want to do. They can intern in a field of their choice to see if they really like it or not. They gain exposure to ‘real world’ social and professional expectations by interacting and communicating with external advisors and their team, which will help them in their lives beyond the school walls. Gaining functional skills in a field they chose will help them get further opportunities to work in that area, talk with professors, or create a product that can be marketed or published.”

Dr. Murthy loves following along on the students’ personal blogs that document their research. “Some of my students are in internships with university labs doing innovative research. I am learning about new techniques and interesting topics that I can introduce in my classes.” It is amazing to see the teacher become the student throughout our students’ Senior Projects.

Explore the project abstracts below and read about some of the monumental work and research these seniors are conducting—some focus primarily on medicinal research, and others on biology, while several have components of both. Any comments and views you can leave on their blogs are encouraged and we appreciate all of the support we’ve seen so far!

(See all Senior Project blogs.)

Senior Projects: Biology/Medicine

Shyamankita C. - Ikaros

Follow Shyamankita’s blog at https://ikarosucsf.wordpress.com/

Ikaros is a transcription protein that is essential to B cell development. We know that Ikaros is a transcription factor that is crucial to the development of B cells. I will be working with mice with the Ik flox/ df4, and mB1-cre +/- or C21- cre +/- genotypes. mB1-cre encodes for the signaling subunit of the B cell antigen receptors and it is only expressed in the very beginning of B cell development. The CD21- cre gene is only expressed in mature B cells. When floxed Ikzf1 is cut out, we are left with 1 of the2 Ikzf1 alleles, which will then either be dF4 (if the mouse had that), or the wt allele. This relates to autoimmunity because studies have shown that autoimmune diseases are associated with SNPs annotated to the Ikaros gene but also the Ikaros gene itself. By using dF4 and mB1-cre/ CD21- cre mice, we can see the role Ikaros plays in B cell development at different stages and how it limits autoimmunity and prevents auto reactive B cells. I will be using Hep 2 Assays and ELIZAs to research Ikaros and its relation to autoimmunity. With my research I hope to begin to clarify the role of Ikaros in B cell development. Research on Ikaros and B cell development could give us more information about autoimmune diseases and therefore lead to better treatment options for them.

Christopher H.  - Stem Cell Competition in Planarian Chimera

Follow Christopher’s blog at https://planariansp.wordpress.com/

The study of stem cells is one of the most medically and scientifically significant fields in biology, as stem cells are crucial to development and regeneration in nearly all multicellular organisms. Planarians, a group of flatworms, are a model organism for studying stem cells. They have an abundance of pluripotent stem cells, which give them the ability to regenerate from nearly any injury. We aim to study planarian stem cells through competition, where distinct groups of stem cells compete within a stem cell niche, or specific environment within the body. Our study organism is Schmidtea mediterranea, a species of planarian with two genetically distinct strains: one that reproduces sexually and one asexually. In order to observe stem cell competition in Schmidtea, we will form chimeral organisms that contain two or more genetically distinct groups of cells, between the two strains. We will be doing this with whole planarians, by cutting the worms lengthwise and fusing on half of one strain with one half of the other. By labeling cells from each half and performing gene knockouts, we can see how the planarians respond to fusion and if there is any specific immune response. This study could also produce interesting insights into the regulatory processes of stem cell and potentially insight into the innate immune recognition and response during tissue transplants.

Steven J. - Molecular Engineering of Organic Dyes Toward More Efficient Sensitizers for Titanium Dioxide Dye-Sensitized Solar Cells.

Follow Steven’s blog at http://www.praisethelorddsscsolarcell.com/

Dye sensitized solar cells utilize photosensitive dyes rather than molecularly-engineered semiconductors as an electron source. The major components of the solar cell are the dye, the semiconductor, the catalyst, and the electrolyte. My research will focus one particular process in the production of photosensitive dyes for a DSSC: the inclusion of an auxiliary acceptor between the donor component and π-bridge in the DSSC dye. My research will begin with the use of natural dyes as model for further calculations and analysis involved with synthetic DSSCs. I will be using porphyrin derivatives as the electron donor component. By the end of my senior project I will have determined whether or not the D-A-π-A motif is superior in photovoltaic efficiency over a D-π-A motif. Improvements in solar technologies have an enormous potential to impact the lives of people worldwide. In particular, renewable energy sources alleviate the energy burden of developing countries, and promising to help address worldwide poverty levels. Overall, renewable sources of energy increase the standard of living for the entire population without incurring substantial costs for the future generations.

Alvin K. - Comparing Current and Previous Innovations in Bone Growth and Healing

Follow Alvin’s blog at https://bonegrowthhistory.wordpress.com/

Bone fractures happen to everyone. No matter what the cause, 2.4 fractures per 100 people occur every year. As such over the years, research has been done to fully optimize the detection and treatment of these fractures. Specifically, within the past 30 or so years, the optimization behind healing fractured bones has accelerated at a rate not seen since the origins of medicine. Between modern innovations in mechanical and material engineering as well as computer simulations to fully model bone stresses and healing, modern technology has revolutionized the way we see bone healing. However, despite the high frequency of this particular type of injury, it is not commonly covered in classes, often being left to specialty courses. By conducting research on the history of these innovations in bone healing, I hope to learn more about the fascinating transition from splints to internal fastening. After conducting my research, I intend to create a research paper that will hopefully allow interested students to dive into a field not often covered in standard biology classes.

Kush P. - Saving Lives on the Verge of an Opioid Overdose Mortality with New Mobile Technologies

Follow Kush’s blog at https://preventopioidoverdoses.wordpress.com/

The concern over the opioid epidemic is quickly increasing. Over 64,000 Americans died from drug overdoses in 2016, with opioid overdose deaths 5 times higher than that of 1999. Many of these deaths are preventable but due to a lack of timely medical intervention, this is often not the case. Therefore, I aim to create a solution to this problem in which help can arrive as soon as possible and save the victim from passing away. The symptoms of an opioid overdose can be identified by three distinct signs often known as the "opioid overdose triad" including pinpoint pupils, unconsciousness, and respiratory depression. My senior project will focus primarily on the pinpoint pupils symptom, which indicate that the pupils in the eye are constricted less than 2mm. Keeping this in mind along with the goal of reducing opioid overdose deaths, I will create a mobile application capable of detecting the symptom of pinpoint pupils and depending on the size of the pupil, alert first responders and close family and friends.

Avani R. - Opioid Therapy Use at UCSF

Follow Avani’s blog at https://reddyforopioids.wordpress.com/

My research is regarding opioid therapy at UCSF. Opioids are a major prescription health care cost, representing 10% of all prescriptions in the US. The proposed health service research project will identify the facilities and VISNs with the largest percentages of high-risk users of opioid therapy and those in which opioid pain medication prescribing practices deviate most from the CPG. Thus, the project will provide the foundation for a planned subsequent implementation project using the ATHENA Opioid Therapy DSS and other interventions to improve provider practices and bring them in closer compliance with the CPG. In addition, the implementation project would be expected to improve health outcomes of patients by enhanced analgesia levels, improved psychosocial functioning and reduced adverse effects and opioid misuse. My research project builds off of what I was working on during my internship at UCSF this summer. Essentially, this summer I worked with a team to extract patient data that would fit the criteria we are looking for: essentially trying to find patients within the UCSF database that have been taking opioids (methadone, oxycodone, fentanyl, and morphine) as medication along with their ICD10 codes that are pertinent to depression, anxiety, drug abuse, drug dependence, and certain results that we were looking into on lab urine drug screens.

Jasper Z. - Marketing Research of a Smart CPR Dummy

Follow Jasper’s blog at https://marketresearchfordummies.wordpress.com/

CPR is one of the most important skills a first responder can master; it can be the difference between life and death. However, CPR is a difficult skill to learn, requiring special training and certification. Currently, CPR dummies are very primitive, molded pieces of plastic that mimic the shape and rigidity of the human chest. The main issue these primitive dummies present is the lack of practice in diagnosing the condition of victims by listening for breathing and feeling for pulse. Currently, CPR instructors must call out scenarios, telling the student when the "victim" is breathing or not, which first responders will not have the luxury of. For my project, I will help create a CPR dummy which will provide useful and relevant feedback. I will also be working with ETALink, a company that specializes in electrical components, to determine how to best implement these features given the limited amount of space available in a CPR dummy.

Amrita B. - The Effectiveness of Drug-Eluting Stents

Follow Amarita’s  blog at https://heartstents.wordpress.com/

As we age, fat deposits build up in the form of plaque in our heart’s major blood vessels. For more than 3 million people in the US, plaque in the coronary artery restricts blood flow to the heart and results in the diagnosis of coronary heart disease. Among the plethora of treatment options is the insertion of a drug-eluting stent in the artery to restore blood flow. Unfortunately, this medical procedure may results in a devastating complication called in-stent restenosis. Restenosis is the re-blocking of an artery due to the inflammation of cells that line the arterial wall. Drug-eluting stents are manufactured to preempt restenosis, but why does it still occur? The Conte Lab is researching new therapeutic targets in both animal models and human subjects to answer this question. My role in the lab includes analyzing data from new drug compounds and their effect on vascular proliferation of endothelial and smooth muscle cell cultures. In addition, I will study the effect of three current drug’s inhibition of cell proliferation. Cell proliferation will indicate whether the drugs are effective in preventing restenosis, an indicator in how effective a certain stent treatment is. The goal is to create a comparative analysis of drugs and their efficacy in preventing complications. This project will help explore advancements in heart stent research and current treatment plans to inform and educate thousands of patients and doctors who consider heart stents annually.

Manaswini G. - Row, Row, Row Your Nanobot

Follow Manaswini’s blog at https://manubots.wordpress.com/

I'm trying to solve whether or not nanorobots are effective in cancer drug delivery after a specific cancer is detected with nanoparticles. Cancer, as we know, is one of the deadliest diseases in the world with no cure to it . Whatever cancer treatments are currently used aren't consistent, they work sometimes and don't work other times, and even when they work they may cause side effects by effecting healthy cells (chemotherapy). Since methods like nanoparticles, nanorobots, and chemotherapy don't produce perfect results individually, I wanted to see if these methods can work flawlessly together. Since this project is theoretical, I will be having many discussions and getting access to data via my Genentech advisor while I'm on the Genentech campus. I hope to find a way to prove that nanoparticles and nanorobots can be combined in some way and can actually be an effective way to treat cancer. I also hope to come up with my own idea to treat cancer after all the reading I am doing and right a mini research paper on that.

Nitya B. - Need a Hand?

Follow Nitya’s blog at https://needahandsrp.wordpress.com/

Robotic grippers are great. Robotic grippers being used for manufacturing in factories are even better. But, how could robotic grippers be controlled directly, without the need for uploading a different program each time there’s a new function it needs to learn? One solution for this is a glove, fitted with sensors, that can feed input to a software that would then replicate those movements on the gripper arm. It's a task that will require ample research, design, and prototyping. To begin this process, I will be researching products currently in use, as well as methods of taking input from said glove and converting it to information that can be used to determine the motions of the gripper. Following that, I will focus on designing the various components, including the basic gripper design, and the set-up for the glove. I will also be learning about how to develop software for the glove using the Arduino and accompanying Arduino software. Using the acquired information, I expect to be able to then further develop my designs for gripper and glove, as well as begin setting up the Arduino to gather input data and control the glove. In the end I expect to have a completed design model with supporting research and I hope to utilize the knowledge and experience gathered from this project to further my interests in engineering and learn more about the research and design process that many engineers go through.

Lorne Z. - Using Machine Learning to Diagnose Lung Cancer Through CT Image Classification

Follow Lorne’s blog at https://lornespblog.wordpress.com/

From Netflix recommendations to Google Home Minis, machine learning is everywhere, giving computers the ability to outsmart, outdo, and outperform humans in countless fields through the use of complex algorithms and neural networks. In medicine, machine learning has the potential to increase diagnosis accuracy and efficiency and discover new drugs. Through this independent investigation, I hope to explore machine learning and apply it to biological topics, specifically lung cancer diagnosis. Due to my limited experience with computer science in general, I will begin my investigation by taking an online machine learning class and training with the MNIST handwritten digit dataset. After the initial learning phase of my project, I will utilize Kaggle's 2017 Data Science Bowl lung cancer dataset to create, train, and test my own machine learning algorithm. Through this project, I hope to build a foundation in computer science, specifically machine learning, as I enter college. I also hope to show how a high schooler with limited computer science experience can enter a complex field such as machine learning.

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